The NCAA stripped Oregon of a scholarship in each of the next two seasons and placed the program on probation for three years, opting against stiffer penalties like a bowl ban despite issuing a show-cause order against former coach Chip Kelly, who apologized to the school, its fans and it players.
The Division I Committee on Infractions released a report Wednesday that found Kelly and the university failed to monitor the program.
The NCAA has been looking into Oregon's recruiting practices since questions arose over a 2010 payment of $25,000 to Willie Lyles and his Houston-based recruiting service, Complete Scouting Services. Lyles had a connection with an Oregon recruit.
"No one wants to be in this position, so I don't think anyone is happy," Oregon athletic director Rob Mullens said. "We're pleased to be at the end of the process."
The committee decided against hitting Oregon with a bowl ban or other major penalties, handing down sanctions that mostly fell in line with those proposed earlier by the university.
"I've not met an institution that wants to go through the infractions and enforcement process," infractions committee member Gregory Sankey said. "This was a multiyear effort that certainly existed, and there are penalties that impacted the program. The committee made its decisions based on information given to it, not on other speculation and evaluations."
Mullens said the school would not appeal.
"The penalties are in place to impact the program and they will impact the program," Mullens said. "It's a very competitive environment for elite level student-athletes."
Oregon faces three years of scholarship reductions, starting last year and extending through 2014-15. It also faces reductions in paid visits and evaluation days, but avoided some of the harsher penalties handed down to other programs in recent years.
Through self-imposed sanctions, Oregon lost one new scholarship in 2012-13 and its total number of scholarships was reduced by one from the maximum of 85. It also will lose a new scholarship in 2013-14 and have the total reduced by one each year through the 2014-15 academic year.
"Even one matters," Mullens said.
The NCAA reduced Oregon's official paid visits from 56 to 37 for the next three academic years, reduced its evaluation days for each of the next three seasons and banned the program from using recruiting services during the probation period.
It also placed an 18-month show-cause order for Kelly, which would require schools wishing to hire him to appear before the Committee on Infractions to determine if the school should be subject to the show-cause procedures. Kelly left Oregon this year to become the coach of the Philadelphia Eagles.
"Now that the NCAA has concluded their investigation and penalized the University of Oregon and its football program, I want to apologize to the University of Oregon, all of its current and former players and their fans," Kelly said in a statement. "I accept my share of responsibility for the actions that led to the penalties.
"As I have I stated before, the NCAA investigation and subsequent ruling had no impact on my decision to leave Oregon for Philadelphia. I have also maintained throughout that I had every intention to cooperate with the NCAA's investigation, which I did.
"I do expect the University of Oregon and its football program to continue to thrive at a high level. They are a talented and resilient group of coaches and players, and I'm sure they will attempt to put today's news behind them very quickly and move forward as they prepare for the 2013 season."
Former assistant director of operations Josh Gibson was given a one-year show-cause order. The NCAA said Gibson was aware of Lyles' involvement in recruiting and commonly told him to tell recruits to contact football coaches.
The Committee on Infractions also found that Lyles provided cash and free lodging to a prospect and engaged in impermissible calls and off-campus contact with prospects, their families and high school coaches.
It also said the football program allowed staff members to engage in recruiting activity, exceeding coaching limits.
The NCAA said Kelly was unaware of Lyles' involvement in recruiting, but the committee noted it is the head coach's responsibility to know the rules and ensure staff and coaches comply with them.
Under Kelly, the Ducks appeared in four straight BCS bowl games -- including a bid for the national championship against Auburn in 2011. Oregon finished 12-1 last season, capped by a victory over Kansas State in the Fiesta Bowl.
Kelly was replaced by offensive coordinator Mark Helfrich, who will make his debut as head coach Aug. 31.
"Throughout this process, there has been speculation and innuendo regarding the nature and severity of potential violations, much of which was unfounded," Mullens said in a statement. "As stated by the NCAA Enforcement Staff, the violations committed in this case were unintentional. The University of Oregon remains committed to fair play, integrity and the best interests of our student-athletes. We have all learned from this experience and look forward to continuing the progress of broad-based excellence in Oregon athletics."
Oregon previously was penalized by the NCAA in 2004 for a major violation involving the improper recruitment of a junior college player by an assistant coach. The university was put on probation for two years, and the unidentified assistant coach was suspended without pay for a week and restricted from some recruiting activities.
The Ducks remained eligible for postseason play and did not lose any scholarships because of that violation, which occurred in 2003.
Information from The Associated Press was used in this report.